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159 results for “human chromosome”
A comprehensive catalog of exact short tandem repeat regions on autosomes and sex chromosomes of the human genome GRCh38
<p>To obtain a general TR catalog across the human genome, we identified genomic intervals with a stretch of exact repetitions of a DNA motif ranging from 1-6bp on GRCh38 autosomes and sex chromosomes by using STRfinder (v1.0), and each STR region was annotated based on gencode.V38 (https://www.gencodegenes.org/human/release_38.html). To end up, we successfully found 1,233,959 TR intervals, covering 0.783306% (24.2 Mbp) of GRCh38 (https://console.cloud.google.com/storage/browser/_details/genomics-public-data/resources/broad/hg38/v0/Homo_sapiens_assembly38.fasta). </p>
Chromosome images used for "Centromere detection of human metaphase chromosome images using a candidate based method"
<p>Chromosome image data used in the paper "Centromere detection of human metaphase chromosome images using a candidate based method". Images are in tiff format</p>
Chromosome images used for "Centromere detection of human metaphase chromosome images using a candidate based method"
<p>Chromosome image data used in the paper "Centromere detection of human metaphase chromosome images using a candidate based method". Images are in tiff format.</p>
Data of: Imputation-free reconstructions of three-dimensional chromosome architectures in human diploid single-cells using allele-specified contacts
<p>These files are results obtained in<br><span><span><span><span>Imputation-free reconstructions of three-dimensional chromosome architectures in human diploid single-cells using allele-specified contacts</span></span></span></span><br>by Yoshito Hirata, Arisa H. Oda, Chie Motono, Masanori Shiro & Kunihiro Ohta.</p> <p>There are 33 files for the corresponding each reconstruction of three-dimensional chromosomone structures<br>for each cell.<br>There are 3D structures for 15 GM cells and 18 PBMC cells, which are obtained from the single cell Hi-C data of Tan et al. Science (2018).</p> <p>For each file, there are 6 columns:<br>The first column corresponds to the allele (0: maternal, 1: paternal)<br>The second column corresponds to the chromosome (1-22: chromosome's number, 23: X, 24: Y)<br>The third column corrsponds to the base point.<br>The fourth column, the fifth column and the sixth column correspond to x-, y-, and z-axes of our reconstruction.</p>
Evaluating homophily of human PPI with respect to chromosomes
<p>Homophily/heterophily evaluation, expressed in terms of z-score values, is related to the human Protein-Protein Interaction Network (PPI), obtained from the STRING v11.5 database (<a href="https://string-db.org/">https://string-db.org</a>) setting standard threshold on edge score (T=700). Each protein occurring in the PPI was assigned to a class corresponding to the chromosome the related gene belongs to.</p> <p>A total of 23 classes (<em>chr1</em>, <em>chr2</em>, ..., <em>chr22</em>, <em>chrX</em>) were considered (excluding the class corresponding to chromosome Y because of the small number of genes occurring in the network).</p> <p>The homophily/heterophily nature of the network, with respect to chromosome classes, was evaluated through HONTO tool (<a href="https://github.com/cumbof/honto">https://github.com/cumbof/honto</a>).</p> <p>In other words, the tendency of proteins to preferentially interact with proteins whose genes are physically located on the same chromosome (homophily) or on different chromosomes (heterophily) was investigated and evaluated in terms of z-scores.</p> <p>Values related to intra (along the diagonal) and inter chromosomal interactions (other than the diagonal) are also reported as a heatmap.</p> <p>As one can observe, values occurring in the diagonal are clearly higher than values out of the diagonal, leading to assess a homophilic nature of the network, confirming the link between shared chromosome and interaction in the PPI.</p>
A comprehensive catalog of approxiamte short tandem repeat regions on autosomes and sex chromosomes of the human genome GRCh38
<p>To obtain a general TR catalog across the human genome, we identified genomic intervals with a stretch of approximate repetitions of a DNA motif ranging from 1-6bp on GRCh38 autosomes and sex chromosomes by using STRfinder (v1.0), and each STR region was annotated based on gencode.V38 (https://www.gencodegenes.org/human/release_38.html). To end up, we successfully found 1,656,159 TR intervals, covering 1.107653% (34.2 Mbp) of GRCh38 (https://console.cloud.google.com/storage/browser/_details/genomics-public-data/resources/broad/hg38/v0/Homo_sapiens_assembly38.fasta). </p>
Figure 2. – A in Transmission of Induced Chromosomal Aberrations through Successive Mitotic Divisions in Human Lymphocytes after In Vitro and In Vivo Radiation
Figure 2. – A: Transverse section of the brown meagre otolith. B: Focus on annual marks (red points).
Figure 1 in Transmission of Induced Chromosomal Aberrations through Successive Mitotic Divisions in Human Lymphocytes after In Vitro and In Vivo Radiation
Figure 1. – Photograph of the proximal (left) and distal (right) sides of the brown meagre sagittae (LT = 497 mm). Scale bar = 1 cm.
Data of: Imputation-free reconstructions of three-dimensional chromosome architectures in human diploid single-cells using allele-specified contacts
Open the record for dataset details and reuse information.
Non-centrosomal microtubules at kinetochores promote rapid chromosome biorientation during mitosis in human cells
<p>Kinetochore tracking data associated with "Non-centrosomal microtubules at kinetochores promote rapid chromosome biorientation during mitosis in human cells" by Renda, Miles, et al., Current Biology, 2022.</p> <p>Contact Alexey Khodjakov at alexey.khodjakov@health.ny.gov for any questions or processing routines.</p> <p>Each file contains coordinates of centrioles and kinetochores in a single cell. </p> <p>Key to variables:</p> <p>ao -- time point corresponding to anaphase onset</p> <p>cell_id -- comprises three parts: cell type_treatment_number (NaN when only first 15 min of prometaphase were tracked).</p> <p>centrioles -- coordinates of centrioles. Two pages correspond to the two centrosomes, first three columns are X-Y-Z of the mother and the second three columns are X-Y-Z of the daughter centrioles</p> <p>kinetochores -- coordinates of kinetochores. Each page corresponds to a chromosome. X-Y-Z coordinates of sister kinetochores are in columns 1-3 and 4-6.</p> <p>neb -- time point corresponding to nuclear envelope breakdown.</p> <p>total_chrs -- number of chromosomes in the cell</p> <p>tracked -- number of tracks obtained in the cell</p>
Chromosome communities in the human pangenome
<p>Results of the analysis of the acrocentric chromosome community in the human pangenome. The plots were presented at the T2T/HPRC assembly meeting on May 9th, 2022.</p>
Bridging the Chromosome-Centric and Biology and Disease Human Proteome Projects: Accessible and automated tools for interpreting biological and pathological impact of protein sequence variants detected via proteogenomics
<p>Bridging the Chromosome-Centric and Biology and Disease Human Proteome Projects: Accessible and automated tools for interpreting biological and pathological impact of protein sequence variants detected via proteogenomics</p>
Tree Sequence and Genealogical Forest Files for a Simulated Human Chromosome 20
<p>Dataset containing 640000 samples simulated using <a href="https://github.com/popsim-consortium/stdpopsim">stdpopsim</a> 0.2.0 and the <code>HapMapII_GRCh38</code> genetic map.<br>The tree sequence was converted to a genealogical forest files via <a href="https://github.com/lukashuebner/gfkit">gfkit</a> version <code>fbd2740</code>.</p>
Supplementary material 1 from: Tonyan ZN, Puppo IL, Saifitdinova AF, Vavilova TV, Glotov AS (2024) Assessment of quadrivalent characteristics influencing chromosome segregation by analyzing human preimplantation embryos from reciprocal translocation carriers. Comparative Cytogenetics 18: 1-13. https://doi.org/10.3897/compcytogen.18.115070
Supplementary information
KaryoCreate: a CRISPR-based technology to study chromosome-specific aneuploidy by targeting human centromeres
GEO Series GSE217325. Homo sapiens. 4 samples. Type: Expression profiling by high throughput sequencing.
Oncogenic lncRNAs alter epigenetic memory at a fragile chromosomal site in human cancer cells [WGS]
GEO Series GSE180957. Homo sapiens. 1 samples. Type: Other.
XIST dampens X chromosome activity in a SPEN-dependent manner during early human development [RNA-seq]
GEO Series GSE246642. Homo sapiens. 30 samples. Type: Expression profiling by high throughput sequencing.
Detect genomic aberrations between PB1 and its counterpart, spindle-chromosome complex in human MII oocyte, PB2 and female pronucleus in human zygote at a single-cell level.
GEO Series GSE56676. Homo sapiens. 4 samples. Type: Genome variation profiling by genome tiling array.
Rapid gain and loss of a chromosome drives key morphology and virulence phenotypes in Histoplasma, a fungal pathogen of humans
GEO Series GSE296938. Histoplasma ohiense. 57 samples. Type: Expression profiling by high throughput sequencing.
Human naïve pluripotent stem cells exhibit X chromosome dampening and X-inactivation (single cell RNA-Seq)
GEO Series GSE87237. Homo sapiens. 288 samples. Type: Expression profiling by high throughput sequencing.
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These curated guides explain access requirements, typical timelines, costs, and reuse considerations for widely used research datasets.
Allen Brain Atlas
Allen Brain Atlas is an Allen Institute collection of brain map atlases, datasets, APIs, and analysis tools covering mouse, human, and non-human primate brain resources.
Annotated Behaviour and Observability Dataset (ABODe)
ABODe is a University of Edinburgh DataShare dataset for behavior classification in group-housed mice using home-cage video, identities, bounding boxes, ground-plate positions, and annotator labels.
DANDI Archive for NWB datasets
DANDI is a BRAIN Initiative archive for publishing and sharing neurophysiology data, including electrophysiology, optophysiology, and behavioral data packaged as NWB and related standards.
International Brain Laboratory public data
The International Brain Laboratory public data releases expose standardized mouse decision-making experiments, including Neuropixels recordings, widefield calcium imaging, behavior, and session metadata accessed through the ONE API.
OpenNeuro
OpenNeuro is a free, open platform for sharing neuroimaging datasets, with public search, dataset pages, and download paths for web, S3, DataLad, and the OpenNeuro CLI.